tbuckley/cabot-search huggingface dataset:
Abstract 461: Mixed supervision to improve the classification and localization: Coherence of tumors in histological slides
Authors: Paul Tourniaire, Marius Ilie, Paul Hofman, Nicholas Ayache, Hervé Delingette
Journal: Cancer Research (2022)

Abstract With the growing standardization of Whole Slide Images (WSIs), deep learning algorithms have shown promising results for the automated classification and localization of tumors. Yet, it is often difficult to train such algorithms, as they usually require careful detailed annotations from expert pathologists, which are tedious to produce. This is why in general only slide-level labels are accessible while annotations of small regions (or tiles) are limited. With only slide-level information, it is difficult to obtain accurate predictions of the localization of pathological tissues inside a slide, despite reaching good slide-level classification. Besides, existing algorithms show limited consistency between slide- and tile-level predictions, leading to difficult interpretation in case of healthy tissue. Using the attention-based multiple instance learning framework, we propose to combine slide-level labels on all slides with tile-level labels on a small fraction (e.g. 20%) of slides within a histology dataset to improve both classification and localization performances. With this mixed supervision of slides, we aim to enforce a better consistency between slide- and tile-level labels. To this end, we introduce an attention-based loss function to further guide the model’s attention on discriminative regions inside tumorous slides, and display an equal attention among all tiles of normal slides. On the Camelyon16 dataset, we reached precision and recall scores as high as 0.99 and 0.85 respectively with an AUC of 0.93 on the competition test set, using only 50% of the slides with tile-level annotations in the training set. Experiments using various proportions of fully annotated slides in the training set show promising results for an improved localization of tumors and classification of slides. In this work, we showed that using a limited amount of fully annotated slides we can improve both the classification and localization performances of an attention-based deep learning model. This increased consistency and performances should help pathologists to better interpret the algorithm output and to focus on suspicious regions in probable tumorous slides. Citation Format: Paul Tourniaire, Marius Ilie, Paul Hofman, Nicholas Ayache, Hervé Delingette. Mixed supervision to improve the classification and localization: Coherence of tumors in histological slides [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 461.
Abstract 2831: High-throughput T cell receptor cloning allows optimization of anti-miHA T cell therapies
Authors: Alexander M. Rowe, Dominic Didiano, Wenzhong Wei, Sawa Ito, Mark Shlomchik, Warren Shlomchik
Journal: Cancer Research (2022)

Abstract Adoptive T cell therapy with CD8+ T cells engineered to express T cell receptors (TCRs) that recognize hematopoietically-restricted minor histocompatibility antigens (miHAs) is an attractive approach for improving the efficacy of allogeneic hematopoietic stem cell transplantation. We developed a mouse model to determine how to optimally implement anti-miHA T cell therapy, focusing on the key characteristics of anti-miHA TCRs that correlate with in vivo efficacy. We immunized B6 mice to the Kb-restricted miHA H60 and used a high throughput approach to amplify TCR α/β chains from single CD8+ MHC Multimer-H60+ (TetH60+) cells. Based on β chain sequencing of 472 single T cells, a broad repertoire was engaged by H60-vaccination, without a clear β chain preference. We randomly chose 178 unique TCRs, cloned them into retroviral backbones and expressed them in a TCR-CD8+ NFAT-reporter reporter cell lines and screened for H60-reactivity by NFAT-induction after stimulation with H60-pulsed antigen presenting cells (APCs). We chose 22 unique TCRs that had clear H60-specific NFAT-induction for deeper characterization. In similarly-transduced 4G4 reporter cells, these TCRs spanned a range of surface expression levels, affinities for H60 as measured by TetH60 binding, and EC50s in response to H60-pulsed APCs (between 1 and 12 μM peptide concentration). We focused initial functional studies on 2 high avidity TCRs (TCR 61 and TCR 167) with EC50s of 1.25 and 2.5 µM, respectively. These were cloned into an optimized retroviral vector and transduced into B6 CD8 cells concomitant with efficient CRISPR-knock out of the endogenous TCRα/β genes. Engineered T cells bound H60 loaded MHC multimers and killed H60+ targets in vitro. The mean TCR expression of transduced cells was 16-30% of that in unmanipulated T cells, though some had TCR expression similar to or greater than that in unmanipulated T cells. We used TCR 61 and 167 transduced T cell products to treat H60+ blast crisis leukemia cells (BC-CML). TCR 61 and 167 T cell products expanded and were equally effective at reducing BC-CML numbers in spleen and bone marrow (BM). Despite having a greater EC50 and equivalent surface expression in reporter cells, when recovered post-transplant, TCR167 cells had higher TetH60 binding, and produced more IFN-γ. Ongoing studies are testing these and additional TCRs alone and in competition to better elucidate TCR properties that predict for in vivo efficacy. Citation Format: Alexander M. Rowe, Dominic Didiano, Wenzhong Wei, Sawa Ito, Mark Shlomchik, Warren Shlomchik. High-throughput T cell receptor cloning allows optimization of anti-miHA T cell therapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2831.
Limited nutrient availability in the tumor microenvironment renders pancreatic tumors sensitive to allosteric IDH1 inhibitors
Authors: Ali Vaziri-Gohar, Joel Cassel, Farheen S. Mohammed, Mehrdad Zarei, Jonathan J. Hue, Omid Hajihassani, Hallie J. Graor, Yellamelli V. V. Srikanth, Saadia A. Karim, Ata Abbas, Erin Prendergast, Vanessa Chen, Erryk S. Katayama, Katerina Dukleska, Imran Khokhar, Anthony Andren, Li Zhang, Chunying Wu, Bernadette Erokwu, Chris A. Flask, Mahsa Zarei, Rui Wang, Luke D. Rothermel, Andrea M. P. Romani, Jessica Bowers, Robert Getts, Curtis Tatsuoka, Jennifer P. Morton, Ilya Bederman, Henri Brunengraber, Costas A. Lyssiotis, Joseph M. Salvino, Jonathan R. Brody, Jordan M. Winter
Journal: Nature Cancer (2022)

Abstract Nutrient-deprived conditions in the tumor microenvironment (TME) restrain cancer cell viability due to increased free radicals and reduced energy production. In pancreatic cancer cells a cytosolic metabolic enzyme, wild-type isocitrate dehydrogenase 1 (wtIDH1), enables adaptation to these conditions. Under nutrient starvation, wtIDH1 oxidizes isocitrate to generate α-ketoglutarate (αKG) for anaplerosis and NADPH to support antioxidant defense. In this study, we show that allosteric inhibitors of mutant IDH1 (mIDH1) are potent wtIDH1 inhibitors under conditions present in the TME. We demonstrate that low magnesium levels facilitate allosteric inhibition of wtIDH1, which is lethal to cancer cells when nutrients are limited. Furthermore, the Food &amp; Drug Administration (FDA)-approved mIDH1 inhibitor ivosidenib (AG-120) dramatically inhibited tumor growth in preclinical models of pancreatic cancer, highlighting this approach as a potential therapeutic strategy against wild-type IDH1 cancers.
Abstract 1609: Oxidative stress triggers tumor edge progression of tumor microenvironment in the minipig spinal cord glioma model
Authors: Kecheng Lei, Muhibullah S. Tora, Stewart G. Neill, Purva P. Nagarajan, Thais Federici, Peter Canoll, Nicholas M. Boulis
Journal: Cancer Research (2022)

Abstract Oxidative stress is exerted by reactive oxygen species (ROS) that accumulate due to an imbalance between ROS generation and elimination, which impacts cellular metabolism and consequently tumorigenesis in the tumor microenvironment. Recently, our group has developed a spinal cord glioma (SCG) model in Göttingen minipigs. However, the mechanism of how SCGs balance redox and thereby modulate cellular proliferation is unclear. Here, we demonstrated that the NRF2/NQO1 signaling, known to mediate oxidative stress, is upregulated in unresectable SCG cells infiltrating at the leading edge compared with the core cells. Moreover, pro-inflammatory cytokines, including TNF-α, IL-1β, and IL-6, were significantly elevated in the edge SCG cells. Immunohistochemistry demonstrated positive staining for a higher Ki-67 proliferative index, GFAP, SOX2 and Olig2 in the edge cells compared to the core cells. The oxidative metabolic heterogeneity of immune and stromal cell subtypes among tumor samples was also explored. Hence, our study demonstrated the tumor microenvironment and involvement of the NRF2/NQO1 pathway for redox homeostasis in our minipig SCG model, which can be used to explore targets of the pre-clinical treatment investigations in SCG. Citation Format: Kecheng Lei, Muhibullah S. Tora, Stewart G. Neill, Purva P. Nagarajan, Thais Federici, Peter Canoll, Nicholas M. Boulis. Oxidative stress triggers tumor edge progression of tumor microenvironment in the minipig spinal cord glioma model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1609.
Abstract 314: Amplifying STING activation by cyclic dinucleotide-manganese particles for systemic cancer immunotherapy
Authors: Xingwu Zhou, Xiaoqi Sun, Wang Gong, Yu Leo Lei, James J. Moon
Journal: Cancer Research (2022)

Abstract Background: Innate immune pathway of stimulator of interferon genes (STING) orchestrates antitumor immune responses and can elicit potent antitumor efficacy. However, clinical development of cyclic-dinucleotide (CDN) STING agonists is mostly limited to intratumoral administration because of the undesirable pharmacological properties of CDN. This limits their applications in treating metastasis, hematologic malignancies, and hard-to-reach solid tumor. Here, we aim to develop a pharmacological formulation that facilitate systemic delivery of CDN STING agonist to broaden its applications for cancer treatment. Methods: Nutritional metal ions physiologically mediate various immune processes, which could potentially be utilized for modulating the STING pathway. By screening different nutritional metal ions, we discovered manganese ion (Mn2+) and cobalt ion (Co2+) synergize with CDN STING agonists and significantly enhance type-I interferon (IFN-I) responses. As Mn2+ has been used in FDA approved drugs, we further developed the formulation to enable systemic codelivery of Mn2+ and CDN. Results: Mn2+ could significantly potentiate the STING activation by up to 77-fold. In addition, Mn2+ interact with CDNs and self-assemble into nanocrystals that could be stabilized as uniform nanoparticles (~120 nm) through lipid layer coating (CDN-Mn Particle, CMP). After either intratumoral or intravenous administrations, CMP effectively elevate the serum levels of inflammatory cytokines (IFN-β, TNF-α, CXCL-9, and CXCL-10), mitigates the suppressive functions of myeloid cells, relieve the immunosuppressive tumor microenvironment (TME), and induce antigen-specific CD8+ T cells expansion. Minute dose of CMP given intravenously exert remarkable antitumor efficacy in CT26, B16F10, and immune checkpoint blocker (ICB)-resistance tobacco-associated NOOC1 murine tumor models, leading to efficient tumor regression. Furthermore, the systemic biodistribution of CMP could be modulated by changing the composition of the lipid layer coating, allowing for organ-specific delivery of CMP to target tumor malignancies in certain organs. Conclusions: CMP provides a novel and versatile platform for local and systemic cancer treatment. More importantly, it highlights the potential of harnessing metal ions in treating various immune-mediated diseases. Citation Format: Xingwu Zhou, Xiaoqi Sun, Wang Gong, Yu Leo Lei, James J. Moon. Amplifying STING activation by cyclic dinucleotide-manganese particles for systemic cancer immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 314.
Abstract 1207: Bento: A toolkit for subcellular spatial analysis of RNA organization
Authors: Clarence Mah, Noorsher Ahmed, Dylan Lam, Hannah Carter, Gene Yeo
Journal: Cancer Research (2022)

Abstract We present Bento, a Python toolkit for subcellular spatial analysis of RNA, implementing tools for ingesting highly-multiplexed spatial transcriptomics data, visualization, detection of RNA localization patterns, identification of cell states, and subcellular spatial statistics. We applied our methods to analyze multiple spatial transcriptomics datasets from a variety of platforms, including seqFISH+ (10k RNA in cultured mouse fibroblast cells) MERFISH (130 RNA in cultured U2-OS cells), and the Spatial Molecular Imager (980 RNA in FFPE of NSCLC and breast cancer tumors) to show how subcellular spatial analysis can be leveraged to understand RNA localization and behavior. We use tensor factorization to perform unsupervised clustering analysis of subcellular patterns in each dataset, demonstrating how cell type and morphology are consistently linked to spatial RNA organization. Citation Format: Clarence Mah, Noorsher Ahmed, Dylan Lam, Hannah Carter, Gene Yeo. Bento: A toolkit for subcellular spatial analysis of RNA organization [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1207.
Abstract 847: Role of RHOA in diffuse gastric cancer tumors
Authors: Agueda Martinez-Barriocanal, Higinio Dopeso, Lizbeth M. Jiménez-Flores, Juliana C. Santos, Estefania Anguita, Josipa Bilic, Rocio Nieto, Elia García-Vidal, Manuel Sánchez Martín, Stefania Landolfi, Kazuto Kobayashi, Javier Hernandez-Losa, Simo Schwartz, Santiago Ramón y Cajal, Diego Arango
Journal: Cancer Research (2022)

Abstract Gastric cancer constitutes the third leading cause of cancer mortality worldwide and tumors with diffuse histology have poor prognosis and low response rates to therapy. Missense mutations in the RHOA (Ras homolog family member A) GTPase have recently been identified in 24% of patients with diffuse gastric cancer. RHOA mutations are not randomly distributed along the coding sequence, but enriched in specific and recurrent hotspots. Substitution in codon 42 (Y42C) occurs in approximately 50% of the patients in which RHOA is mutated. RHOA orchestrates cellular processes such as proliferation, differentiation, migration and invasion, whose deregulation is essential for the onset, maintenance and progression of tumors. However, the functional role of wild type RHOA and RHOA mutants remains poorly characterized in gastric cancer. We used isogenic cell lines systems and animal models to study the impact of RHOA in the gastric tumorigenesis. RHOA loss strongly increased the proliferation, migration and invasion of diffuse gastric cancer cells in vitro, but also when growing as subcutaneous xenografts in immunodeficient mice, and in experimental mouse models of peritoneal and lung metastasis. Stomach tumor burden was also increased in transgenic mice conditionally expressing a dominant negative form of RHOA in the gastrointestinal tract (RHOA T19N). Moreover, cells overexpressing wild-type RHOA or G14V RHOA (a constitutive active form of the GTPase) exhibited reduced tumorigenic features both in vitro and in vivo. Conversely, diffuse gastric cancer cells engineered for overexpressing RHOA Y42C mutant, displayed enhanced growth and invasion in vitro. Importantly, stomach cancer tumors formed more efficiently in a transgenic mouse model in which we targeted the expression of Y42C RHOA mutant to the gastric epithelium. Collectively, these results demonstrate that RHOA has tumor-suppressive activity in diffuse gastric cancer, while the recurrent Y42C hotspot RHOA mutation found in these tumors is oncogenic. Citation Format: Agueda Martinez-Barriocanal, Higinio Dopeso, Lizbeth M. Jiménez-Flores, Juliana C. Santos, Estefania Anguita, Josipa Bilic, Rocio Nieto, Elia García-Vidal, Manuel Sánchez Martín, Stefania Landolfi, Kazuto Kobayashi, Javier Hernandez-Losa, Simo Schwartz, Santiago Ramón y Cajal, Diego Arango. Role of RHOA in diffuse gastric cancer tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 847.
Abstract 2832: Identifying tumor specific surface protein markers for glioblastoma immunotherapy by single-nuclei RNA-seq
Authors: Omar M. Ibrahim, Liang-Bo Wang, Lijun Yao, Wagma Caravan, Nataly Naser Al Deen, Reyka G. Jayasinghe, Milan G. Chheda, Li Ding
Journal: Cancer Research (2022)

Abstract Glioblastoma (GBM) is one of the deadliest adult brain tumors, in which the typical treatments of surgery, chemotherapy, and/or radiotherapy yield generally poor median survival. GBM is categorized into IDH-mutant subtype and IDH-wildtype subtype, which is subcategorized into proneural, classical, and mesenchymal subtypes, yet few personalized treatment options are available. The use of genetically modified chimeric antigen receptor T cells (CAR-T), such as CD19 CAR-T, has shown significant clinical efficacy in the treatment of hematological malignancies due to specific antitumor response; however, CAR-T response in GBM has been poor. Single nuclei RNA-seq (snRNA-seq) technology offers high-resolution profiling of different cell populations and their specific differential patterns. Accordingly, we developed a robust genomic analysis pipeline that can be applied to external datasets, tumor, and healthy samples. This was followed by unbiased systematic analysis of GBM tumor-specific cell surface markers using 18 single nuclei RNA sequencing (snRNA-seq) samples to identify GBM specific CAR-T targets allowing efficient tumor cells targeting and minimum off-target effects by CAR-T (1). We identified key potential targetable cell surface-specific markers and we also identified subtype-specific targets. Our findings provide insights into tumor-specific cell surface proteins that may be potential targets for engineered immunotherapy. References:(1) Wang, Liang-Bo, Alla Karpova, Marina A. Gritsenko, Jennifer E. Kyle, Song Cao, Yize Li, Dmitry Rykunov, et al. "Proteogenomic and metabolomic characterization of human glioblastoma." Cancer cell 39, no. 4 (2021): 509-528. Citation Format: Omar M. Ibrahim, Liang-Bo Wang, Lijun Yao, Wagma Caravan, Nataly Naser Al Deen, Reyka G. Jayasinghe, Milan G. Chheda, Li Ding. Identifying tumor specific surface protein markers for glioblastoma immunotherapy by single-nuclei RNA-seq [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2832.
Abstract LB192: Demethylation, DNA damage and antitumor activity of DNA methyltransferase inhibitors in models with intact and disrupted DNMT1 gene
Authors: Angelo B. Laranjeira, Melinda Hollingshead, Dat Nguyen, Robert Kinders, Michael Difilippantonio, James H. Doroshow, Sherry X. Yang
Journal: Cancer Research (2022)

Abstract DNA methyltransferase (DNMT) 1 is an enzyme responsible for maintaining DNA methylation pattern during DNA replication. However, its role on the methylation of tumor suppressor genes and DNA damage in relation to antitumor activity of DNMT inhibitors remains controversial. Here, we investigated the effects of DNMT inhibitors in human colorectal and breast cancer cell lines and animal models with intact (DNMT1+/+) and disrupted DNMT1 (DNMT1-/-) gene. Treatment with 5 µM of 4’-thio-5-aza-2’-deoxycytidine (aza-TdC), decitabine and azacytidine all inhibited DNMT1 expression and cell growth (94.0%/97.1%, 39.9%/58.6% and 69.2/91.3), and induced apoptosis (66.9%/62.5%, 30.9%/23.8% and 66.2/43.1%) in DNMT1+/+ HCT116/MCF7 cells; in contrast, the DNMT inhibitors had less/little activities in DNMT1-/- HCT116/MCF7 cells (P&amp;lt;0.001 each). γH2AX and G2/M cell-cycle arrest were induced by the inhibitors and greater degree of induction was produced by aza-TdC than decitabine in DNMT1+/+ cells (P&amp;lt;0.001), with activation of checkpoint kinase 1 and upregulation of p21. Both demethylation and increased acetylation of CDKN2A and CDKN2B gene promoters together with re-expression of p16INK4A and p15INK4B proteins were detected in DNMT1-/- versusDNMT1+/+ (demethylation only) cells upon exposure to decitabine for 72h. Compared with saline treatment, tumor growth was significantly inhibited by aza-TdC (90%; n=18 mice) and decitabine (62%; n=18) in DNMT1+/+ colorectal xenograft tumors, alongside decreasing expression of DNMT1 (51% and 44%) and an increase in p21 (85% and 48%). Similarly, tumor growth delays (86%; n=15 and 57%; n=14) were associated with the reduction of DNMT1 and augmentation of p21 in bladder PDX tumors. The findings suggest that DNMT inhibitors induce DNA damage and higher anti-tumor activity of aza-TdC is proportional to a greater magnitude of induction of DNA damage, p21 and cell cycle arrest without reactivating the expression of p16INK4A and p15INK4B. The gene re-expression coupled to demethylation and acetylation corresponds to the less anti-tumor activity by decitabine in DNMT1-/- cells. Thus, it is the DNA damage effects, rather than re-expression of the tumor suppressors, that are associated with antitumor activity of the DNMT inhibitors in cancer cells and/or xenograft and PDX tumors. Citation Format: Angelo B. Laranjeira, Melinda Hollingshead, Dat Nguyen, Robert Kinders, Michael Difilippantonio, James H. Doroshow, Sherry X. Yang. Demethylation, DNA damage and antitumor activity of DNA methyltransferase inhibitors in models with intact and disrupted DNMT1 gene [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB192.